Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model

Tuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC–MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.


Streptomycin 2nd
Antibiotic 11 1.0 20,21,60 25 73 7 73 Mutations to genes that dictate the shape of ribosomal protein S12 (rspL) or 16 s ribosomal RNA (rrs) [74][75][76] as well as inhibitory mutations of a 16S ribosomal RNA methyl transferase (gidB) 77,78 Amikacin 2nd Semi-synthetic Antibiotic 79 0.5-2.2 20,21,80 17 79,81 17 79,81 Mutations to the genes that dictate the shape of 16S ribosomal RNA (rrs) [82][83][84] and loss of function mutations on the gene for a ribosome methyltransferase (tlyA) 85 Kanamycin A 2nd Antibiotic 11 1.0-5.0 21,60,65,86 8 87 5 87 Mutations to the genes that dictate the shape of 16S ribosomal RNA (rrs) [82][83][84] and mutations in the promoter region of the gene for an N-acetyltransferase that plays a role in cell survival (eis) 88 www.nature.com/scientificreports/ wise, the semisynthetic compound, amikacin is derived from kanamycin A via an acylation reaction with L-(-)-4-amino-2-hydroxybutyric acid which is not detected in the human metabolome 12 . Therefore, because amikacin cannot be produced biosynthetically without additional synthesis of L-(-)-4-amino-2-hydroxybutyric acid, it is excluded. Of the twelve first-and second-line therapies, only capreomycin IA/IB, D-CS, kanamycin A, streptomycin, and Rifamycin SV could be produced in human cells because their precursors were present in human cells and their pathways are fully biosynthetic. Between those pathways, D-CS is the shortest pathway requiring only six steps for synthesis (Table 1). In contrast, capreomycin IA/IB requires fourteen steps, kanamycin requires eight steps, streptomycin requires twenty-five steps, and Rifamycin SV requires twenty-seven steps. D-CS is a second-line antibiotic capable of treating multidrug-resistant TB and is produced by several Streptomyces species 13 . S. lavendulae produces D-CS using L-serine, acetyl-CoA, L-arginine, and six enzymes encoded by DcsABCDEG (Fig. 1). This biosynthetic pathway has been heterologously reproduced in Escherichia coli and was shown to synthesize micromolar concentrations of D-CS 14 . Additionally, D-CS inhibits two essential enzymes for bacterial cell wall synthesis, alanine racemase and D-alanyl-D-alanine ligase 15 , which contributes to the lowresistance incidence to D-CS 16 . Because D-CS is synthesized in a relatively short pathway, the precursors are present in human cells, and there is a low resistance incidence 16 , the D-CS pathway is optimal for the proposed genetic chemoprophylaxis.

A549 cells express soluble and insoluble DcsE-FLAG-GFP.
We sought to test if DcsE, the first enzyme of the S. lavendulae D-CS biosynthetic pathway, is functional when synthesized in human cells. To express DcsE-FLAG-GFP in human lung (A549) cells, we transfected the cells with plasmid DNA containing DcsE-FLAG-GFP or FLAG-GFP as a negative control. GFP fluorescence can be used as a measure of whether DcsE is expressed and its location within the cell. Following twelve hours of transfection, we observed diffuse GFP fluorescence in the FLAG-GFP transfected cells (Fig. 2a). In contrast, we observed both diffuse GFP fluorescence as well as puncta in the DcsE-FLAG-GFP transfected cells (Fig. 2b). Based on these observations, we conclude DcsE-FLAG-GFP expresses in A549 cells.
Detection of L-OAS using HPLC-MS/MS. We developed a method to detect L-OAS and the reactants in a reaction buffer suitable for DcsE using HPLC-MS/MS. We observed specific retention times for L-serine at 0.9 min (Fig. 3a), L-OAS at 1.1 min (Fig. 3b), and acetyl CoA ( Fig. S1) with masses that correspond to L-serine and L-OAS (Figs. 3c-f). A parent ion of an L-serine standard yielded a mass of 106.049 m/z and fragments into a mass of 88.0396 m/z which is consistent with the loss of an alcohol group (Fig. 3e). A parent ion of an L-OAS standard yielded a mass of 148.06 m/z with three fragment ions of 130.05 m/z (consistent with the loss of an alcohol group from L-OAS), 106.049 m/z (consistent with the loss of the acetyl group on L-OAS), and 88.0396 m/z (consistent with the loss of an alcohol group from deacetylated serine; Fig. 3f). A pure L-serine standard reveals only a mass for L-serine at 0.9 min (Fig. 3c). A pure L-OAS standard reveals masses of both L-serine and L-OAS at the retention time of 1.1 min with no serine peak at 0.9 min (Fig. 3b,d). This observation is consistent with deacetylation of the L-OAS standard into L-serine by the electrospray ionizer following HPLC elution. If serine were present in the original L-OAS standard, a separate retention time would have been observed.
To test if de-acetylation by ESI affects the quantification of L-OAS, we compared the ratio of L-serine peak area (at 1.1 min) and L-OAS peak area (at 1.1 min) across our L-OAS standard curve. We observed that the fragmentation of L-OAS into L-serine is proportional to concentration (Fig. 3g). Therefore, our method is suitable for L-OAS detection and quantification (Fig. 3h). www.nature.com/scientificreports/ Heterologous DcsE-FLAG-GFP catalyzes reaction of L-serine and acetyl-CoA to O-acetyl-L-serine in Vitro. After observing expression of DcsE-FLAG-GFP in A549 cells, we sought to determine if L-OAS could be detected from the transfection media. Media from A549 cells expressing DcsE-FLAG-GFP and FLAG-GFP as a negative control was analyzed using HPLC-MS to detect L-OAS. L-OAS was not detected from the media of cells transfected with DcsE-FLAG-GFP compared to FLAG-GFP (Fig. 4). In both samples, a mass of 148.058 m/z was detected with similar relative abundance (Fig. 4b,c), however, insufficient fragment ions associated with an L-OAS standard (Fig. 3f) were identified (Fig. 4d,e). A fragment of 130 m/z was detected from the FLAG-GFP transfection media indicative of a loss of an alcohol group from the compound with a mass of 148 m/z; however, the serine peak (106 m/z) and the serine fragment ion were not detected (Fig. 4d).
No fragment ions were detected from DcsE-FLAG-GFP transfection media indicating that the compound with a mass of 148 m/z was not L-OAS (Fig. 4e). Taken together, we conclude L-OAS could not be detected from the transfection media.
To understand if DcsE-FLAG-GFP produced in A549 cells is capable of catalyzing the reaction of L-serine and acetyl-CoA to form L-OAS, we purified the enzyme from cells using the FLAG tag. To determine if FLAG-GFP and DcsE-FLAG-GFP were purified following immunoprecipitation, we performed immunoblot analysis on whole cell lysate and select fractions from immunoprecipitation (see materials and methods and  www.nature.com/scientificreports/ To test if purified DcsE produced in A549 cells can catalyze the reaction of L-serine and acetyl-CoA to L-OAS, we reacted L-serine and acetyl-CoA in the presence of purified DcsE-FLAG-GFP or FLAG-GFP as a control and used HPLC-MS to detect the expected product L-OAS. We observed L-OAS in the sample containing DcsE-FLAG-GFP but not FLAG-GFP (Fig. 6a). L-OAS produced by DcsE-FLAG-GFP had a retention time of 1.117 min (Fig. 6a) and 148.0606 m/z (Fig. 6c). Tandem MS shows L-OAS produced by DcsE-FLAG-GFP fragments into 131.0335, 106.0498, and 88.0395 m/z fragments (Fig. 6d), consistent with the tandem MS data for an L-OAS standard (Fig. 3f). No L-OAS was detected in the FLAG-GFP reaction (Fig. 6b). Simultaneously, we ran a standard curve of L-OAS (Fig. 3h) to calculate the L-OAS produced by DcsE-FLAG-GFP. We observed DcsE-FLAG-GFP produced 40.3 µM L-OAS after a 1 h reaction at 30 °C. From this we conclude active heterologous production of DcsE-FLAG-GFP in A549 cells.

Discussion
In this study, we observed that human lung cells transfected with DcsE-FLAG-GFP are capable of synthesizing functional DcsE, which catalyzes the first step towards D-CS synthesis. D-CS is an optimal candidate for a genetic chemoprophylaxis against TB because it is the shortest known pathway for an anti-TB antibiotic with biologically available precursors (Table 1). DcsE tagged with FLAG-GFP can be expressed in A549 cells (Fig. 2), but there is no appreciable difference between the L-OAS detected from DcsE-FLAG-GFP and FLAG-GFP transfection media (Fig. 4). However, purified DcsE-FLAG-GFP (Fig. 5) catalyzes the formation of L-OAS from L-serine and acetyl-CoA (Fig. 6). L-OAS produced by purified DcsE-FLAG-GFP has the expected retention time of 1.1 min (Fig. 6a), a mass of 148.13 m/z (Fig. 6c) and produced the same 106 m/z and 131 m/z fragments at 5 V (Fig. 6d) as the 0.5 mM L-OAS standard in reaction buffer (Fig. 3f). No L-OAS was detected from a reaction containing purified FLAG-GFP (Fig. 6b).
Production of an active DcsE enzyme in human lung cells demonstrates progress towards a genetic chemoprophylaxis against TB. Previous studies have shown that other TB antibiotics such as isoniazid can be used prophylactically to prevent TB infection in those infected with HIV and people who have tested positive for TB by Tuberculosis skin test 26 . Isoniazid is not the only TB antibiotic used chemoprophylactically; rifampicin, pyridoxine, and combinations of rifampicin and pyridoxine have also been shown to reduce the incidence of TB infection compared to a placebo 27 .
One limitation to using D-CS for the proposed gene therapy is the comparatively high minimal inhibitory concentration (MIC) for Mtb of 10-50 µg/mL which could restrict the efficacy of the therapy depending on how much D-CS can be produced in humans. In this study, 40.3 µM L-OAS was produced after a 1 h reaction at 30 °C which equates to 5.94 µg/mL L-OAS, meaning the concentration of a precursor is lower than the MIC of D-CS. Furthermore, no L-OAS was detected in media from FLAG-GFP and DcsE-FLAG-GFP transfected cells (Fig. 4), so DcsE and other D-CS biosynthetic genes needs to be optimized.
However, D-CS expression does not need to reach the full MIC concentration to be effective. Typically, D-CS does not reach MIC concentrations in patients, suggesting reaching MIC is not required for therapeutic efficacy. D-CS is known for its poor lung cavity penetration; the clinical dose for adults of 250 mg only reaches concentrations of less than 2 µg/mL in the lung 28 meaning that small amounts of D-CS being produced intracellularly while infection is mild could be clinically relevant. Future experiments in conditions that more closely model the complex environment of the human system could better determine realistic concentrations of D-CS that could be produced. For example, noncancerous cell models such as Beas-2B, macrophages, and in vivo models could be used. Additionally, in vivo models will better portray how local D-CS expression could protect at the organ level in body systems.
To safely apply genetic chemoprophylaxis for TB, we propose developing an excisable gene therapy that delivers D-CS specifically in the presence of TB infection as depicted in Fig. 7. Such a gene therapy will need to be excisable in the case of adverse effects, inducible in the case of infection, and active specifically in response to TB. The site-specific recombination of the CRE/loxP1 system could be used to permanently excise dcsAB-CDEG in the case of adverse effects. As visualized in Fig. 7a, expression of the recombinase CRE is activated by the drug tamoxifen 29 . When expressed, CRE cleaves the two loxP sites thus excising the construct responsible for production of D-CS (Fig. 7b). The CRE/loxP1 system is a suitable system for this application because it is precise, controlled by a pharmaceutical that is not naturally present in human cells, and is able to stop D-CS expression quickly and permanently. Additionally, dcsABCDEG will be selectively expressed in the presence of infection through an appropriate infection responsive promoter element (InfRE; Fig. 7c). For instance, the MIP-2 promoter could be used to activate the plasmid in the presence of intracellular bacteria such as Mtb 30,31 . Because the MIP-2 promoter is responsive to all intracellular infections, additional molecular engineering will be necessary. To accomplish this, the MycP1 protease 32 , produced by Mtb, could be used to control the expression of www.nature.com/scientificreports/ functional enzymes. By tethering DcsABCDEG with the MycP1 specific polypeptide SLKPASAGGG, we expect active enzyme will only be produced in the presence of TB. By including an infection induced promoter, MycP1 sites between each enzyme to control functionality of enzymes in the presence of TB, and an excisable plasmid controlled by CRE/loxP1 in our design, the expression of D-CS synthesis genes is controlled. Another important safety factor is tolerance by the host. As depicted in Fig. 1, DcsA and B synthesize hydroxyurea from L-arginine 14 . Hydroxyurea is known to be cytotoxic to human cells between concentrations of 2-10 mM 33 . While these concentrations far exceed expected in vivo concentration of D-CS of approximately 50 µM, an important future area of study will be to determine if hydroxyurea reaches toxic levels, or is consumed quickly enough by DcsD to avoid any cytotoxic effects.
The system used to deliver the genetic chemoprophylaxis must be long lasting and well tolerated. Adenoassociated viruses (AAV) are one way to deliver a construct similar to the one proposed in Fig. 7a. AAV are a versatile and effective way of delivering genetic material via a protein shell containing single stranded DNA 34 . The genome capacity of AAV is generally considered to be around 4.5-5 kb which is below the estimated size of the plasmid proposed in Fig. 7. However, AAV5, a serotype of AAV, has been shown to incorporate genome www.nature.com/scientificreports/ sizes up to 8.9kb 35 which is larger than the plasmid proposed in Fig. 7. Cationic liposomes (CLs) are another example of a technology capable of delivering a gene therapy. CLs are non-viral and use a closed lipid bilayer membrane to deliver genes and protect the DNA from degredation 36 . CLs are very customizable and can transfer up to 1,000kb 36 into cells making them another promising technology for gene therapy applications. Overall, both AAV and CLs are delivery methods that could be used to deliver the construct tissue specifically, safely, and dependably. In vivo delivery of gene therapy is an active area of research to increase the relatively low transfection efficiency using AAV and CL 37 . Additionally, future studies would be necessary to determine if macrophages or lung cells would be a better ultimate target for this approach based on the nature of TB infection and the transfection efficiency of each cell type. By observing heterologous production of functional DcsE-FLAG-GFP, we provide evidence that the first step for prophylactic D-CS synthesis is possible in human cells. Our immediate future directions include developing a method to observe this enzymatic activity in live A549 cells and eventually advance to synthesizing all six enzymes in the D-CS pathway via the proposed plasmid. Additionally, future studies could replicate this study in noncancerous cell models such as Beas-2B or macrophages. Finally, in vivo models would ultimately be necessary to determine the efficacy of the proposed genetic chemoprophylaxis. Overall, with the rapid growth of cell-based therapies, we seek to create the tools now to prepare for a future state where gene therapies are commonplace, safe, economically plausible, and well accepted.

Materials and methods
Cell lines and cell culture. Cloning GFP-FLAG-DCSE. The DcsE gene is present in the D-cycloserine synthesizing bacterium Streptomyces lavendulae. S. lavendulae (ATCC #11,924) was obtained from ATCC in freeze dried form, and was reanimated according to supplier instructions (ATCC, n.d.-c). The organism was revived in yeast malt extract broth (5 g dextrose, 2.5 g peptone, 1.5 g malt extract, and 1.5 g yeast extract made up to 500 ml in diH2O) and streaked on the same agar media, with growth occurring two days after inoculation at 26 °C. www.nature.com/scientificreports/ A fresh liquid culture of S. lavendulae was then cultured from a single colony, and following growth, the cells were lysed. 5 ml of cells were pelleted and washed in 200 µl of lysozyme digestion buffer. Then, the cells were transferred to a screw cap centrifuge tube containing 0.1 mm glass beads and homogenized for 30 s. Genomic DNA was then extracted from the bacteria using the PureLink Genomic DNA Minikit (catalog #k182001). The final eluted solution was analyzed using a nanodrop and revealed the clean peak at 260 nm characteristic of DNA. Two concentration readings were performed yielding an approximate concentration of 15 ng/ µl. DcsE was first cloned into the vector pCOOFY50 (Addgene plasmid #55,189) by Gibson assembly (https:// www. nature. com/ artic les/ nmeth. 1318 ) using the NEB HiFi DNA system (catalog # E2621S). 20 ng of PCOOFY50 backbone was amplified using the primers AB0001 and AB0002 (Table 2) and pHusion high-fidelity polymerase (NEB # M0530S) according to the PCR protocol described in Table 3. Likewise, a DcsE fragment was amplified using 50 ng of genomic DNA from S. lavendulae and primers AB0009 and AB0010 using the same protocol. After PCR product cleanup using the Zymo clean and concentrator kit (Zymo #D4004), homologous ends of the two products were annealed using the NEB HiFi DNA system (catalog # E2621S) and transformed into DH5α E. coli as described below.
Neither DcsE nor GFP expressed using the pCOOFY50 vector, so DcsE was subcloned into pCS2 + (https:// www. addge ne. org/ vector-datab ase/ 2295/ ) containing FLAG-GFP downstream of the CMV promoter. DcsE was subcloned into pCS2 + using PCR amplification followed by Gibson assembly as described above with the following modifications: Primers ASB001 and ASB002 were used to amplify pCS2-FLAG-GFP backbone and

Plasmid purification for transfection
To transform competent DH5α with DcsE-FLAG-GFP or FLAG-GFP, 50 µl of competent DH5α and 2 µl of purified plasmid were combined and incubated on ice for 30 min. Samples were heat shocked at 42 °C for 45 s and placed on ice for 5 min. 800 µl SOC was added and shaken for one hour at room temperature. 150 µl of this solution was plated on LB agar plates with 100 µg/ml ampicillin and grown overnight at 37 °C. One colony was transferred to 5 mL sterile LB broth with 100 µg/ml ampicillin and shaken at 37 °C for 12 h. The ZymoPURE Plasmid Miniprep Kit was used following the centrifugation protocol to purify pure plasmid.

Transfection of DcsE-FLAG-GFP. To transfect A549 cells with DcsE-FLAG-GFP or FLAG-GFP, cells
were plated on tissue culture treated 60 mm plates at a concentration of 176,800 cells/mL in complete F-12 K Medium. 12 h after plating, cells were transfected using Lipofectamine 3000 (Thermo Fisher L3000) and 6ug purified plasmid following the Thermo Fisher guidelines for A549 cells 39 . Cells were transfected overnight for 12 h at 37 °C at 4.5% CO 2 . Following 12 h of transfection, media was collected saved for subsequent analysis.
Imaging transfected cells. A549 cells were imaged 12 h following transfection using a Nikon Eclipse TE2000-U inverted phase contrast microscope (Tokyo, Japan) with a Nikon TE2-PS100W power supply, a Chiu Technical Corporation 100-W mercury lamp (Kings Park, USA), and Nikon NIS-Elements software. Cell images were taken using the 10X objective, the 1.5X bonus zoom, and phase 1. For each position, an image was taken using differential interference contrast (DIC) to focus the cells and blue light to image GFP fluorescence. ImageJ was used to merge images.
Preparation of lysate. A549 cells were lysed immediately following transfection and imaging. Media was removed and cells were washed with 5 mL PBS (ATCC 30-2200). 150 µl cold radioimmunoprecipitation assay buffer (RIPA) lysis buffer containing 150 mM NaCl, 1% IGEPAL CA-630 (NP40), 0.5% sodium deoxycholate, 0.1% SDS (sodium dodecyl sulphate), 50 mM Tris-HCl, pH 8.0 was added to each plate. Cells were lysed on ice for about 30 s using a cell scraper. An inverted microscope was used to ensure all cells were lysed. All the liquid was transferred to prechilled microcentrifuge tubes and centrifuged at 13,000xg for 10 min at 4 °C. The supernatant was transferred to a new tube and purification immediately followed.

DcsE-FLAG-GFP lysis and purification.
Cell lysate was immediately purified to remove proteases in crude lysate. Protein was purified using Sigma Monoclonal ANTI-FLAG M2 Affinity Gel and the sigma protocol "Immunoprecipitation of FLAG Fusion Proteins Using Monoclonal Antibody Affinity Gels" was followed. TBS (0.5 M Tris HCl, pH 7.5, 1 M NaCl) was used to wash gel prior to immunoprecipitation. Samples were eluted three times using 3 × FLAG peptide (Rockland Immunochemicals) at a working concentration of 150 ng/µL in TBS. After elution, samples were filtered using 500 µl 10 kDa microcentrifuge filter (Amicon) to filter out excess 3 × FLAG peptide, exchange lysis buffer to 10 × reaction buffer containing 40 mM Tris-HCl (pH 7.6), 400 mM NaCl, 2 mM EDTA, modified from and to concentrate samples to a final volume of 50 µl.
Immunoblotting. Presence of FLAG-GFP and DcsE-FLAG-GFP were detected using the abcam Western blot protocol 40 . 7 µl of each fraction was loaded per lane along with 2.5 µl 4 × LDS sample buffer (Thermo Fisher NP0007). 5 µl PageRuler prestained protein ladder was used as a reference (Thermo Fisher 26,616) A NuPAGE 4-12% Bis-Tris Gel (Thermo Fisher NP0321BOX) was used with NuPAGE MES SDS running buffer (Thermo Fisher NP0002) according to the manufactures instructions 41 . Gels were transferred to a PVDF membrane using a Bio-Rad Trans-Blot SD Semi-Dry Transfer Cell at 25 V for 30 min with Bjerrum Schafer-Nielsen Transfer buffer: Tris Base 48 mM and Glycine 39 mM (pH 9.2). The membrane was blocked in 3% BSA (w/v) in PBS 0.1% Tween 20. Primary anti-FLAG (Sigma F1804) was diluted 1:1000 in 3% BSA and the secondary anti-Mouse (Thermo Fisher 31,431) was diluted 1:10,000. ECL substrate (BioRad 1,705,062) was used according to manufac- Table 3. Cycling conditions for gradient PCR. Reactions were run as needed, and ranges of annealing temperature were tested (see table 3 for annealing temperatures used). www.nature.com/scientificreports/ turer's instructions 42 with a BioRad ChemiDoc Imaging System. Western blots were stripped and reprobed using the abcam stripping for reprobing protocol 43 . Primary anti-Tubulin (NOVUS NB600-936) was diluted 1:1000 and secondary anti-Rabbit (Promega W401B) was diluted 1:2000. The blots were imaged as described above.
In vitro L-OAS synthesis. To perform in vitro L-OAS synthesis 14 , 20 µl of purified DcsE-FLAG-GFP and FLAG-GFP were reacted in a 50 µl reaction at a final concentration of 1 mM L-serine, and 1 mM acetyl-CoA in a reaction buffer 44 containing 4 mM Tris-HCl (pH 7.6), 40 mM NaCl, 0.2 mM EDTA, and 1 mM dithiothreitol (DTT). Samples were reacted for 1 h at 30 °C.
HPLC mass spectrometry. HPLC-MS was used to detect L-serine and L-OAS from In vitro L-OAS synthesis samples. Samples were separated using an Agilent 1290 Infinity II HPLC with an YMC ODS-AQ 2.0 mm × 100 mm, 5 μm (YMC America) aqueous C18 column and an Agilent 6545 Quadrupole Time of Flight LC/MS mass spectrometer in positive mode at the Integrated Molecular Structure Education and Research Center (IMSERC) facilities at Northwestern University. 1 µl of samples were injected starting with a concentration of 100% solvent A (H 2 O + 0.1% formic acid (FA)) and 0% solvent B (ACN + 0.1% FA). The ratio of solvent B was linearly increased to 50% from 2.0 to 7.0 min. From 7.0 to 9.0 min the ratio of solvent B was again linearly increased to 99%. From 11.0 min to 11.5 min solvent A was increased from 1.0% to 100%. Solvent A remained at 100% until the total method reached 16 min. The flow rate was set to 0.3 mL/min and all samples were run at room temperature. This method was used to create a standard curve of 1:1 serial dilutions for L-serine and L-OAS ranging from 500 uM to 3.9 uM. Reacted samples were prepared by adding an equal volume of 0.1% FA (Sigma 5.43804) in acetonitrile (Sigma 34,851) immediately after reaction completion. Samples were vortexed and centrifuged at top speed for 10 min and then 75 µl of the supernatant was transferred to autosampler vials. Using the same method as above, HPLC-MS was used to detect product in samples.

Data availability
The underlying data for this work are available from the corresponding author upon reasonable request.